{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,7]],"date-time":"2026-02-07T16:24:22Z","timestamp":1770481462156,"version":"3.49.0"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1490,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The prediction of receptor\u2014ligand pairings is an important area of research as intercellular communications are mediated by the successful interaction of these key proteins. As the exhaustive assaying of receptor\u2014ligand pairs is impractical, a computational approach to predict pairings is necessary. We propose a workflow to carry out this interaction prediction task, using a text mining approach in conjunction with a state of the art prediction method, as well as a widely accessible and comprehensive dataset.<\/jats:p>\n               <jats:p>Among several modern classifiers, random forests have been found to be the best at this prediction task. The training of this classifier was carried out using an experimentally validated dataset of Database of Ligand-Receptor Partners (DLRP) receptor\u2014ligand pairs. New examples, co-cited with the training receptors and ligands, are then classified using the trained classifier. After applying our method, we find that we are able to successfully predict receptor\u2014ligand pairs within the GPCR family with a balanced accuracy of 0.96. Upon further inspection, we find several supported interactions that were not present in the Database of Interacting Proteins (DIPdatabase).<\/jats:p>\n               <jats:p>We have measured the balanced accuracy of our method resulting in high quality predictions stored in the available database ReLiance.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/homes.esat.kuleuven.be\/~bioiuser\/ReLianceDB\/index.php<\/jats:p>\n               <jats:p>Contact: \u00a0yves.moreau@esat.kuleuven.be; ernesto.iacucci@gmail.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts391","type":"journal-article","created":{"date-parts":[[2012,9,7]],"date-time":"2012-09-07T20:35:22Z","timestamp":1347050122000},"page":"i569-i574","source":"Crossref","is-referenced-by-count":5,"title":["ReLiance: a machine learning and literature-based prioritization of receptor\u2014ligand pairings"],"prefix":"10.1093","volume":"28","author":[{"given":"Ernesto","family":"Iacucci","sequence":"first","affiliation":[{"name":"1 IBBT Future Health Department\/ESAT-SCD, KU Leuven, Kasteelpark Arenberg 10, 3001, Heverlee-Leuven, Belgium"}]},{"given":"L\u00e9on-Charles","family":"Tranchevent","sequence":"additional","affiliation":[{"name":"1 IBBT Future Health Department\/ESAT-SCD, KU Leuven, Kasteelpark Arenberg 10, 3001, Heverlee-Leuven, Belgium"}]},{"given":"Dusan","family":"Popovic","sequence":"additional","affiliation":[{"name":"1 IBBT Future Health Department\/ESAT-SCD, KU Leuven, Kasteelpark Arenberg 10, 3001, Heverlee-Leuven, Belgium"}]},{"given":"Georgios A.","family":"Pavlopoulos","sequence":"additional","affiliation":[{"name":"1 IBBT Future Health Department\/ESAT-SCD, KU Leuven, Kasteelpark Arenberg 10, 3001, Heverlee-Leuven, Belgium"}]},{"given":"Bart","family":"De Moor","sequence":"additional","affiliation":[{"name":"1 IBBT Future Health Department\/ESAT-SCD, KU Leuven, Kasteelpark Arenberg 10, 3001, Heverlee-Leuven, Belgium"}]},{"given":"Reinhard","family":"Schneider","sequence":"additional","affiliation":[{"name":"2 Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Limpertsberg, 162 A, avenue de la Fa\u00efencerie, 1511 Luxembourg, Germany"}]},{"given":"Yves","family":"Moreau","sequence":"additional","affiliation":[{"name":"1 IBBT Future Health Department\/ESAT-SCD, KU Leuven, Kasteelpark Arenberg 10, 3001, Heverlee-Leuven, Belgium"}]}],"member":"286","published-online":{"date-parts":[[2012,9,3]]},"reference":[{"key":"2023012513062026200_B1","doi-asserted-by":"crossref","first-page":"W393","DOI":"10.1093\/nar\/gki354","article-title":"TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis","volume":"33","author":"Aerts","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012513062026200_B2","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1093\/nar\/29.1.242","article-title":"BIND\u2013The Biomolecular Interaction Network Database","volume":"29","author":"Bader","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"2023012513062026200_B3","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1080\/08916930802095210","article-title":"Gene expression profiles at different stages of collagen-induced arthritis","volume":"41","author":"Booth","year":"2008","journal-title":"Autoimmunity"},{"key":"2023012513062026200_B4","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/gb-2003-4-5-p3","article-title":"DAVID: Database for Annotation, Visualization, and Integrated Discovery","volume":"4","author":"Dennis","year":"2003","journal-title":"Genome Biol."},{"key":"2023012513062026200_B5","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1038\/415141a","article-title":"Functional organization of the yeast proteome by systematic analysis of protein complexes","volume":"415","author":"Gavin","year":"2002","journal-title":"Nature"},{"key":"2023012513062026200_B6","doi-asserted-by":"crossref","first-page":"2039","DOI":"10.1093\/bioinformatics\/btg278","article-title":"Inferring protein interactions from phylogenetic distance matrices","volume":"19","author":"Gertz","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012513062026200_B7","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1039\/C1MB05340J","article-title":"Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis","volume":"8","author":"Goel","year":"2012","journal-title":"Mol. 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